Not sure what is going on, but it seems that GeneProductAssociations are not written to SBML.
import libsbml
sbmlns: libsbml.SBMLNamespaces = libsbml.SBMLNamespaces(3, 1)
sbmlns.addPkgNamespace("fbc", 3)
doc: libsbml.SBMLDocument = libsbml.SBMLDocument(sbmlns)
doc_fbc: libsbml.FbcSBMLDocumentPlugin = doc.getPlugin("fbc")
doc_fbc.setRequired(False)
model: libsbml.Model = doc.createModel()
model_fbc: libsbml.FbcModelPlugin = model.getPlugin("fbc")
model_fbc.setStrict(True)
c: libsbml.Compartment = model.createCompartment()
c.setId("c1")
c.setSize(1.0)
c.setConstant(True)
s1: libsbml.Species = model.createSpecies()
s1.setId("s1")
s1.setCompartment("c1")
s1.setInitialConcentration(1.0)
s1.setConstant(False)
s1.setHasOnlySubstanceUnits(False)
s1.setBoundaryCondition(False)
p1: libsbml.Parameter = model.createParameter()
p1.setId("lb")
p1.setValue(-100)
p1.setConstant(True)
p2: libsbml.Parameter = model.createParameter()
p2.setId("ub")
p2.setValue(100)
p2.setConstant(True)
# Support exists for user constraints
r: libsbml.Reaction = model.createReaction()
r.setId("r1")
r.setReversible(True)
r.setFast(False)
r_fbc: libsbml.FbcReactionPlugin = r.getPlugin("fbc")
r_fbc.setUpperFluxBound("ub")
r_fbc.setLowerFluxBound("lb")
reactant: libsbml.SpeciesReference = r.createReactant()
reactant.setSpecies("s1")
reactant.setConstant(True)
reactant.setStoichiometry(1.0)
gp1 = model_fbc.createGeneProduct()
gp1.setId("g1")
gp1.setLabel("g1")
gp2 = model_fbc.createGeneProduct()
gp2.setId("g2")
gp2.setLabel("g2")
gpa: libsbml.GeneProductAssociation = r_fbc.createGeneProductAssociation()
gpa.setId("r_gpa")
gpa.setName("r_gpa")
gpa.setAssociation("g1 and g2", True, False)
print("required attributes:", gpa.hasRequiredAttributes())
print(gpa.toSBML())
sbml_str: str = libsbml.writeSBMLToString(doc)
print("-" * 80)
print(sbml_str)
print("-" * 80)Results in
required attributes: True
<fbc:geneProductAssociation fbc:id="r_gpa" fbc:name="r_gpa">
<fbc:and>
<fbc:geneProductRef fbc:geneProduct="g1"/>
<fbc:geneProductRef fbc:geneProduct="g2"/>
</fbc:and>
</fbc:geneProductAssociation>
--------------------------------------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version3" level="3" version="1" fbc:required="false">
<model fbc:strict="true">
<listOfCompartments>
<compartment id="c1" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="s1" compartment="c1" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="lb" value="-100" constant="true"/>
<parameter id="ub" value="100" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="r1" reversible="true" fast="false" fbc:lowerFluxBound="lb" fbc:upperFluxBound="ub">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1" constant="true"/>
</listOfReactants>
</reaction>
</listOfReactions>
<fbc:listOfGeneProducts>
<fbc:geneProduct fbc:id="g1" fbc:label="g1"/>
<fbc:geneProduct fbc:id="g2" fbc:label="g2"/>
</fbc:listOfGeneProducts>
</model>
</sbml>
The GeneProductAssociation just does not appear in the SBML despite added ?!
This probably also solves #253, because the association is set successfully but just not written to SBML.
Not sure what is going on, but it seems that GeneProductAssociations are not written to SBML.
Results in
The GeneProductAssociation just does not appear in the SBML despite added ?!
This probably also solves #253, because the association is set successfully but just not written to SBML.